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How do I do this?

could you extract track that precedes data track (Track 01 usually) with IsoBuster and take a look at it with hex editor, please?
what does 1st and last data sectors (i mean those at the end, from 2nd part of gap) look like in there?

Should the pregap for track 1 be showing as 2 seconds in EAC?

yes, usually
only a couple of Audio CDs had it different so far, i think

What is the swapping method?

basically you prepare drive so cover can be removed freely, then place Audio CD in tray, let drive detect it,
wait until it stops spinning, without ejecting tray remove cover and replace Audio CD with one you are going to extract
and put cover back on, so drive still thinks its an CDDA and will process your CD this way -
as one continuous stream of audio data (so no gaps at all and it will allow to read as far as TOC of Audio CD goes)
it's described in more detail here
except you don't need special Trap CD - any fairly large Audio CD should work
and extraction can be done with IsoBuster

On the Ys IV sample disc, track 1, all data from the start to 18735 (decimal) is zeroed. All data from 7063856 until the end is also zeroed.

By the way, track 1 is not the warning track commonly found in Japanese games. It's actually the English warning track found in US releases.